There is no more significant
process in the biological world than the process of development. It is
found wherever there are multicellular, complex animals and plants, such
as trees and human beings. Without it there would be no such organisms.
It is the engine that drives the changes from fertilized egg, through
sexually mature adulthood, continuing through senescence, and eventually,
to death. It has made each one of us what we are biologically. When developmental
processes go seriously wrong the dreadful results are usually clearly
evident. Development is a truly fundamental, ubiquitous process in the
biologic world.

For all its significance,
however, talk about development does not light up people's eyes. It does
not generate strong passions the way the word, evolution, does. Despite
the wonders it performs most people have only a vague idea of what development
is or does. Development may only signify children to those of us who have
raised a family or are in the process of doing so, with all the satisfactions
and frustrations that accompany it. Although every adult among us is the
product of development this fact does not help us understand development
in a conceptual way as the term will be used in this book.

Development, moreover,
occupies an important but only a narrow, specialized niche in the domain
of biological research and theorizing. By tradition and current practice,
research on development is limited to changes that take place in individual
organisms; more specifically, to those transformations that occur in the
embryonic stages of an organism's life span. Such studies are producing
astounding results in clarifying how the embryo changes on the road to
sexual maturity, and will undoubtedly eventually produce practical results
from which everyone will benefit.

But is that enough?
The answer given in this book is no. Much more should be asked of the
concept of development. The book will take the wraps off the concept,
stretching it over the entire life span rather than just the embryonic
period; and even further, applying it to how large groups of animals and
plants acquired the shapes they have over long periods of geologic time.
Development, expanded to its full potential, will be shown to be the master-shaper
of life, both individually and historically.

The concept of development
needs a historical dimension because, as this book will show, it is development,
not evolution, that sculpted the fundamental "shape" of organic
life from deep history of organic life to the present. This will be done
by offering evidence that development is the dynamo that drove physical
and anatomical changes in the major groups of genetically continuous animals
and plants (called phyla) from the Cambrian explosion over the past 530
million years. This historical dimension of development will provide a
second opinion, so to speak, to the diagnosis of organic life given by
"Dr." Charles Darwin, showing that his assessment of how species
originated is only partly correct. First, however, it is necessary to
indicate how the concept of development can be rationally lifted from
its present limited, individual platform to an expanded historical, world-stage
.

Development
as a Historical Process

What is development?
We begin with the concept of individual development. It is the complex
process whereby a fertilized egg becomes transformed into a sexually mature
adult, and which then eventually declines into a senescent organism that
eventually dies. Development will be seen as an end-directed, programmed,
internally driven, hierarchically regulated process which results in well-defined
temporal sequences and patterns of morphological changes throughout the
total life-span of an organism.

The definition makes
a significant point. Development is a process that covers the entire life
span of an individual organism, not just the embryonic period. Thomson1
supports this view. He wrote, "[Development] begins with the union
of the germ cells and ends only with death." (Italics added). Development
thus defined as a life-long process, departs from the traditional view
which limits it to the early stages of the life cycle. The expanded perspective
advanced herein makes possible new insights into and interpretations of
the individual life span and also of the history of organic life.

This extended definition
of development, moreover, finds empirical support that lends credibility
to its conceptual basis. Evidence is forthcoming which provisionally shows
that some chronic diseases which do not appear until late in a person's
life may have originated in the embryonic period.2

A spate of recent
reports suggests that conditions in the womb may play a role in the
risk of prostate cancer, heart disease, diabetes, high blood pressure,
and other chronic diseases. Such ailments don't appear until the fifth,
sixth, or even seventh decade of life.

That some age-related
diseases may have their origin in embryonic conditions supports the view
that development not only starts early but also ends late-at the end of
the life span.

Even the expanded,
life-long framework of development, however, is still too restricted for
purposes of this book. The concept of development needs further expansion
into an intergenerational process, extending from one generation into
the next. This view is also supported by Thomson3 who said,

The processes of
development form a continuum that begins with gametogenesis and ends
only with the death of the individual organism.All the accumulated history
of the clade to which the individual belongs, everything that is expressed
in the phenotype and anything that is present but unexpressed, all these
are brought together by the processes of development (Italics added).

The time-unit of development
is two generations. Since development spans two generation, it can span
any number of them, and thus becomes a continuous, intergenerational process.
This book will take the position that development stretches back in time,
connecting generations almost without end, back to the dawn of multicellular,
complex animals of modern design that erupted on planet earth 530 million
years or more ago. In this manner the concept of development can be rationally
extended into a deep, historical process.

The above discussion
supports a major claim made in this book, i. e., that principles of
development can be applied not only to changes in individual organisms
throughout their entire life span, but also to progressive transformations
which occurred in phyletic lineages over geologic time, as revealed in
studies of the fossil record. Development is therefore not a process
that starts and stops with individual organisms. It is also the continuous
process that changes the shapes of ancestral, phyletic lineages from which
individual developmental processes are inherited generation after generation.
Development, with this deep historical dimension, will be called phylo-development.

What is the relationship
between individual development and phylo development? It is this: Individual
development is inherited from phylo development. All individual development
that occurs now, or that transpired in the past, or will come about in
the future, finds its origin in the phylo-development. Individual organisms
are the continuously-formed "carriers" of phylo-development;
the sex cells of individual organisms carry the genetic future of the
lineage, even as their somatic cells carry the genetic information that
forms them as an individual organism. Both sex cells and somatic cells
have their origin in the germ line.

It must be clear,
therefore, that although the study of phylo-development starts with individual
organisms, phylo-development did not originate with them. Individual organisms
are the carriers of phylo-development, not the causes of it.

Methodological
Considerations

Individual development,
moreover, produces distinct patterns that may be called the fingerprints
of development. They are the property of development just as our fingerprints
belong to us and no one else. No other biological processes leaves the
same imprint. Once identified and classified the individual fingerprints
become the model for detecting and matching parallel developmental prints
in the past life histories of phyletic lineages. Since the patterns of
individual development are as unique as a person's fingerprints, the analogy
strengthens the assumption that individual patterns can indeed be used
as reliable and valid sign posts of phylo-development in the fossil record.

Phylo-development
may be likened to the author of the history of organic life; individual
development is the editor. As a paper weight shaped like the statue-of-liberty
is a model of the Statue of Liberty in New York harbor, so individual
development is a model of and derived from phylo development. Individual
patterns are inherited and secondary; they are derived from the much more
fundamental, primary process of phylo development in the phyletic lineage.

A brief survey of
basic developmental patterns in individual organisms will be presented
in the next two chapters. Once identified, these individual patterns will
be matched with patterns and transformations in the fossil record.

Definition of
phylo-development. A comprehensive, historical definition of phylo-development
can now be given. It holds that principles and patterns of development
apply to all biological systems, regardless of their size, temporal duration,
or the number of generations spanned. Development is an end-directed,
programmed, internally driven, hierarchically regulated process which
results in determinate temporal sequences and patterns of morphological
changes and occurs (1) in all individual, complex, multicellular organisms
throughout their entire life spans, and (2) in all ancestral lineages
throughout their entire life histories. The terms macro-, ancestral,
phyletic, historical, and large scale, development can be used interchangeably.

Earlier Theoretical
Formulations

Two prior formulations
of the relationship of phyletic and individual development and of long-term
trends in the fossil record will be presented here and will be shown to
be only distantly related to phylo development. The first is the biogenic
law, and the second is orthogenesis.

The Biogenic
Law. Phylo-development is not a warmed-over version of the so-called
the biogenic law, popularized by the slogan, "ontogeny recapitulates
phylogeny." This outmoded "law of recapitulation", formulated
by Ernst Haeckel (1834-1919), held that there is a one-to-one correspondence
between phylogeny and ontogeny; that each organism in its development
from zygote to adult repeats its phyletic history in condensed form, i.
e., climbs its own family tree, so to speak.4 Raff5 described the biogenic
law more technically as follows, "all animals should recapitulate
their phylogenies in an abbreviated form during development, and developmental
stages should reveal those histories."

Phylo-development,
however, is not concerned with trying to find replications of exact stages
of phyletic transformation in the development of individual organisms;
rather, it focuses on generalized processes and patterns that are universal
across all lineages. What is inherited from phylogeny, is first, the process
of development itself, and second all the patterns and principles found
in individual development, not the supposed stages that appeared previously
in ancestral ontogenies.

Orthogenesis.
Phylo-development is distantly related to ideas were held in the 1920s
by several paleontologists. Eldredge6 reported the situation as follows:

Paleontologists
have had an abiding interest in long-term evolutionary trends that struck
Cope and many others as linear or "rectilinear." "Orthogenesis,"
a term coined by Haacke (1893; fide Simpson 1944), describes a pattern
of linear directional change in phylogeny, a pattern generally thought
in presynthesis days to reflect internal evolutionary processes. This
line of thinking, at least in paleontological circles, reached its culmination
in the work of vertebrate paleontologist Henry Fairfield Osborn, whose
theory of orthogenesis (later called "aristogenesis") saw
linear evolutionary change arising from within organisms themselves,
a mechanism, moreover, taking precedence over natural selection if not
supplanting it altogether .

The general theory
of phylo-development is an advance over the earlier ideas of "orthogenesis"
and "aristogenesis" because it (1) is a multidimensional concept;
it identifies many different kinds of long-term trends that are parallel
to individual development, and because it (2) relates the process to real
causal genetic mechanisms, as will be treated in detail in later chapters.
Such concrete biological explanations were lacking in the earlier concepts.

Analogical reasoning.
The phylo-developmental framework adopted herein involves a degree of
analogical reasoning, which uses a known process (individual development)
to predict a larger, unknown process (phylo development). Individual development
is the analog for phyletic development in this book. Olson7 described
the utility of analogies in physics as follows:

Analogies are useful
for analysis in unexplored fields. By means of analogies an unfamiliar
system may be compared with one that is better known. The relations
and actions are more easily visualized, the mathematics more readily
applied, and the analytical solutions are more readily obtained in the
familiar system.

Darwin knowingly used
analogical reasoning in arguing for the reality of natural selection.
He chose selective breeding of animals, called artificial selection or
domestic breeding, as his analog of natural selection. His analogy contains
an obvious defect, however, in that artificial selection is guided by
an external human agent, i.e., the breeder, and therefore is based on
the purposes and choices of the breeder. The dog fancier chooses what
characteristics he/she wishes the dog to have-long ears, short legs, etc.,-and
selects the offspring that most nearly approximates the goal for future
breeding.

Natural selection,
however, has no such external, intelligent guide. No distant goals drive
natural selection, it is guided only by what enhances immediate survival,
adaptation, and procreative success. It is purposeless; the Blind Watchmaker,
as Dawkins8 called it. Darwin's analogical reasoning was criticized by
his contemporaries not because of this large flaw but because he used
nature and natural selection metaphorically.9

Individual development,
the analog for historical, phylo-development, is a stronger analogy than
Darwin's because individual development is a bona fide, naturalistic,
biological process, not one in which an intelligent human intervention
plays a part. It is, moreover, physically and causally related by heredity
to the larger process of phylo-development and thus is much more than
a mere analogy.

An analogy provides
only the first exploratory step in a scientific work. It generates hypotheses.
Individual development thus generates hypotheses about what to expect
phylo-development. The second step is explanation, which analogy cannot
supply. In this book, principles of development will be used to describe
trends and morphological patterns found in the fossil record, which will
be explained and accounted for by the causal mechanisms of genetics and
inheritance.

The Structure
of the Genetic System

The structure of the
genetic system provides a mechanistic basis for a comprehensive theory
of development. It has two interconnected domains represented by the somatic
genome, found in individual organisms, and the germ line, that connects
genetically continuous groups of animals. The role of the somatic genome
in individual development will be introduced below and treated in detail
in later chapters.10

The somatic genome
contains the "library" of genetic information for the life-long
development and maintenance of the individual organism. Found in every
cell of the body (soma) it, along with non-genetic controls (called epigenetic
controls) also found in every cell, provides major regulation of the processes
of individual development. It is inherited from the germ line of the lineage,
lasts for one generation, and then perishes with the death of the organism.

Individual organisms,
from the historical perspective, are significant to an ancestral lineage
primarily because they provide nurturing and protective housing for the
all-important germ line as mentioned above. As Samuel Butler is reported
to have observed, a hen is the egg's way of producing another egg. The
germ line found in the egg, (or, more accurately, the sex cells found
in hens and cocks), contains genetic information and epigenetic controls
for future generations of chickens as well as for the next individual
bird.

Development, as a
process (the total sequence of regulatory events), is inherited along
with anatomical structures (e.g., nervous systems and livers), morphological
patterns (e.g., hoofs and beaks), and some behavior patterns (e.g., nocturnal
hunting). Inheritance provides the connecting link and continuity between
ancestral development and individual organisms. For the historic patterning
and continuity of the lineage the germ line is of critical importance,
to which the reader's attention is now directed.

The germ line contains
the "central library," so to speak, of genetic information that
will produce the major developmental features of the entire phyletic lineage;
and loans books, so to speak, to the individual's somatic genomic library.
This metaphor expresses a central theme of phylo-developmental theory,
namely, that the phyletic germ line is programmed with specific structural
and regulatory genetic information that shapes the basic architecture
of the lineage, i. e., its major morphological and anatomical features,
such as the body plan. This view is in sharp distinction from Darwinian
evolutionary theory which holds that the germ line is unprogrammed.11
The central library metaphor, however, can easily accommodate unprogrammed
Darwinian concepts when the data demand it, such as natural selection.
Just as modern libraries add new books to their collections, and are equipped
with copy machines, so Darwinian mechanisms can copy, change, and add
new genetic information to the basic pre-programmed germ line.

The core collection
of the central library was not stocked recently nor was it supplied instantaneously
with information. The process may have began as long as 1.0-1.2 billion
years ago, deep in the Precambrian, and reached a "critical mass"
of genetic information at about 530-525 million years ago, in the Early
Cambrian, at which time an unprecedented explosion of 50 or so stem animals
occurred with novel, individually unique body plans or body architecture;12
each of the stem animals being the founder of a phylum. "The Cambrian
may have been a period in which the genetic programs that control embryonic
body plans locked into the forms we now recognize," wrote Levinton.13

According to the developmental
perspective, the central library was highly organized, with its information
divided and subdivided into sections. Thus the phyletic germ line of each
stem animal was differentiated and segregated into suites or modules of
genetic programs along with their controlling regions. As a given phyletic
germ line unfolded after the Cambrian explosion, it produced a lineage
whose long journey through geologic time was shaped like a step-pyramid
in Egypt, descending in step-wise fashion from the topmost stem animal
into ever lower, more specific, and widening categories of the lineage.
That is, the control was hierarchical. The body plan of the stem animal
at the top constrained the offspring in the next lower category, the second
lower category controlled all those below it, etc. These progressively
descending, more specific steps are called taxonomic levels of the lineage
that help scientists classify animals and plants. The phyletic germ line
continued to be differentiated and segregated and expressed in this fashion,
descending ever more specifically through classes, order, families, genera,
clear down to species, at which point the last programs of the lineal
germ line were completely played out. This phylo developmental process
resulted in the multiplicity of species found in the present time, numbering
by some estimates, from 5 million to 50 million,14 but which have not
produced any new, higher level organisms.15

The above scenario
suggests further that the phyletic germ line may have originated, perhaps
as sets of highly ordered genes, such as the Hox genes, and other regulatory
and structural genes, tucked away in relatively simple, undifferentiated,
Precambrian proto-animals. The existence of such animals is purely hypothetical
at this point, since no fossils of them have been found. How the germ
line of each phylum arose is still a mystery; any scenario proposed to
explain it is largely speculative at the present time. Perhaps because
of their high degree of order and efficient repair mechanisms, the germ
lines of the proto-animals were presumably comparatively resistant to
mutations; hence the absence of empirical evidence of natural selection
at work and the observed dearth of species in the Early Cambrian.

Disorder in the germ
line, expressed as progressive mutability and instability, doubtless increased
incrementally with each lower taxonomic differentiation from the top down,
until today, after hundreds of millions of years, it is most pronounced
at the level of species. Species multiply because the lineal germ line
is more mutable and variable, more influenced by the environment, thus
making Darwinian natural selection possible. No wonder that there are
so many species today. But on the dark side, disorder in the germ line
also presages the gradual decline and aging of lineages.

This view of phylo-development
introduces a major insight into the Origin of Species and where Darwin
went wrong. Phylo-development holds that the observed phyletic trend is
downward, from the topmost taxonomic categories to the lowest-species.
Species have their origin in higher taxonomic levels of the lineage and
also in sister species. Species signal that the lineage has arrived at
the end of the line. Because speciation is so rampant today, however,
Darwin assumed, and his followers followed suit, that species are and
always have been the beginning of phyletic lineages. They all assumed
that species are the origin of lineages, which then supposedly rise to
higher taxonomic levels; i. e., that phyletic lineages evolve upwards.
Not so. Such upward trends have never been observed, and never will be
according to the developmental perspective because lineages develop from
the top down.

The direction of phyletic
trends and implications for phylo-development and Darwinian evolution
will be presented in great detail in chapter five.

The Strategy
of the Book: Science, the Search for Patterns, Processes, and Mechanisms

This book is a scientific
document. Science is an attempt to understand the world in naturalistic,
empirical terms. Within this naturalistic framework, science will be viewed
in this book as a three-tiered search suggested by Thomson16-the search
for observable patterns, underlying processes, and causal
mechanisms in developmental phenomena.17 The search will be driven
by the attempt to provide a scientific understanding of phylo-development.
The remainder of the book will present and review evidence for key paleontological
and biological patterns and causal mechanisms in support of the process
of phylo development.

Patterns, Processes,
and Causal Mechanisms

A pattern
refers to a design, or theme found in a biological system. Two kinds of
developmental patterns are significant: 1) the physical shape, size, and
proportion (morphology) of an organism and its parts; 2) and temporal
sequences, steps, or trends, that exhibit regularity in the course of
development. The concept of patterned directionality is important for
phylo-development. It is possible thus to speak of a trend, a vector,
or direction of change in development as a pattern because it changes
in a regular, sequential manner.

Patterns lie closest
to raw data; they are inferred from raw data. Patterns may also embody
principles of development.

Processes.
Processes underlie patterns and consist of internal biological activities
and interactions with the environment that occur in accordance with general
regularities or laws of nature and that produce characteristic observable
patterns. Processes can be inferred from patterns because patterns imply
underlying correlated processes-order, regularities, rules, and principles.
Examples of biological processes are found in individual development,
phylo-development, and natural selection. Each produces characteristic
associated patterns.

Causal mechanisms
are agents or accepted theories or laws that explain the processes in
question. It is generally held "that the occurrence of an event is
explained when it is subsumed under or covered by a law of nature, i.e.,
when it is shown to have occurred in accordance with some general regularity
of nature."18 Biological mechanisms, at the most fundamental level,
explain processes at the intermediate level, which in turn are correlated
with patterns at the most observable level. Causal mechanisms need to
be identified to round out the full scientific understanding of processes
and patterns.

Genetic and epigenetic
information encoded in the programs in the somatic genome of individual
organisms, and the genetic and epigenetic information in the germ line
are the causal agents for the general theory of phylo-development.

4 Martin, E. A., Dictionary
of Life Sciences (New York, Pica Press, 1984), pp. 315-316. Martin's description
continues, "For example, a mammal starts life as a single cell, resembling
its protozoan ancestors, then becomes a two-layered embryo, resembling
a coelenterate ancestor, and later goes through a stage having gill slits
similar to its fish ancestors."

5 Raff, R., The Shape
of Life (Chicago, The University of Chicago Press, 1996), p. 2.

10 It must be understood
from the outset that genetics provides only part of the story of development.
"There cannot be a genetic theory of morphology," according
to Miklos, "nor a genetic theory of morphological evolution, because
gene expression itself is under epigenetic control". Miklos, G. L.
M., "Emergence of organizational complexities during metazoan evolution:
perspectives from molecular biology, palaeontology and neo-Darwinism."
Mem. Ass. Australas. Palaeontols (1993 15, 7-41. ISSN 0810-8889), p. 30.
Epigenetic control refers to control of gene expression that lies outside
the genetic machinery; it is found rather, in other constituents of the
cell, cell surface molecules, controlling regions in cells, signals from
neighboring cells, feedback loops. Less is known about epigenetic controls,
however, than about the how genes produce various embryonic structures.
Developmental genes, moreover, are modular . They work more as teams than
as individual players.

11 Raff, R., The Shape
of Life (Chicago, The University of Chicago Press, 1996), p. 30.

15 An allegedly new
phylum was recently discovered. Whether it will given status in the list
of confirmed phyla remains to be seen. See Funch, P. Kristensen, R. M.,
"Cycliophora is a New Phylum with Affinities to Entoprocta and Ectoprocta"
Nature 378 (December 14, 1995), pp. 711-714.